A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
example_isolates_unclean
A data.frame with 3,000 observations and 8 variables:
patient_id
ID of the patient
date
date of receipt at the laboratory
hospital
ID of the hospital, from A to C
bacteria
info about microorganism that can be transformed with as.mo(), see also microorganisms
AMX:GEN
4 different antibiotics that have to be transformed with as.rsi()
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.
On our website https://msberends.github.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!